EPA proposes overhaul of water permit sign-off rules

On January 15, 2026, the U.S. Environmental Protection Agency (EPA) proposed revisions to the Clean Water Act (CWA) regulations with the intention of limiting state and tribal abilities to block projects through water quality permitting. Specifically, EPA proposed to revise Section 401 water quality certification regulations to “restore Section 401 to its proper statutory purpose” by narrowing the scope of review, clarifying timelines, and introducing uniform submission requirements. EPA says the changes will improve efficiency and reduce delays, as delays and refusals to grant Section 401 certifications have long been a strategy employed by state and tribal authorities to prevent projects they disfavor from moving forward.

Key takeaway

The proposed rule narrows the scope of review to discharges, standardizes what must be included in certification requests and decisions, and tightens timing provisions to prevent delays. EPA aims to create a more predictable, and uniform Section 401 framework that reduces uncertainty for applicants while preserving states’ and Tribes’ core water‑quality protection responsibilities.

Section 401: Why it matters

Currently, Section 401 of the Clean Water Act requires applicants for federal permits or licenses that may result in a discharge to waters of the United States to obtain a certification or waiver from the relevant state, authorized Tribe, or (in limited circumstances) EPA ensuring compliance with water quality standards and other appropriate requirements of state law. Certifying authorities may grant, grant with conditions (which are then incorporated into the federal authorization), or deny certification, and must act within a reasonable period of time not to exceed one year or the requirement is waived. Once the federal agency receives both the application and a certification, it must promptly notify EPA under the neighboring-jurisdiction process in CWA Section 401(a)(2), and it may not issue the license or permit until that process is complete. 

Some major federal licenses and permits subject to Section 401 include: 

• EPA-issued CWA Section 402 permits for discharge of pollutants,
• FERC certificates for construction/operation of interstate natural gas pipeline projects,
• River and Harbors Act Section 10 permits for construction of wharfs and piers,
• Nuclear plant licenses issued by Nuclear Regulatory Commission, and
• Section 404 permits for the discharge of dredged or fill materials into waters, including wetlands by U.S. Army Corps of Engineers.

Key proposed changes

1. Narrowed scope of review: EPA proposes limiting Section 401 review to whether point‑source discharges into waters of the United States will comply with applicable water quality requirements. This means certifying authorities may not base decisions on broader project impacts or non‑water‑quality considerations.
2. Standardized requirements for certification requests: EPA would establish one national, exclusive list of information required to start the statutory review clock, removing state and tribal authority to add additional mandatory elements. EPA warns that states cannot “blur the bright-line rule” for when the 1‑year clock begins. N.Y. State Dep’t of Envtl. Conservation v. FERC, 884 F.3d 450, 455-56 (2d Cir. 2018).
3. Clarified timelines: EPA proposes to eliminate automatic extensions for state notice procedures or force majeure and prohibit certifying authorities from asking applicants to withdraw and resubmit requests to avoid the one‑year deadline.
4. Required content for certification decisions: Each certification decision to grant, conditionally grant, deny, or expressly waive must: (1) be in writing; (2) state whether the discharge will comply with water quality requirements; (3) for conditions, include an explanation and specific citation to the water‑quality requirement; and (4) for denials, identify the water‑quality requirement that would be violated or specify what information is missing.
5. Modifications: Post‑issuance modifications would require written agreement by the certifying authority, the federal agency, and the applicant.
6. “May affect” process: Simplifies how EPA decides whether a project’s discharge may affect waters in another state. If EPA concludes there may be an impact, the affected state will have to explain why and point to the specific water‑quality rule it believes the project would violate. Federal agencies would also need to finish the objection-and-hearing process within 90 days to prevent delays. 

Regulatory context

The 2026 revision proposal represents the latest adjustment in a cycle of regulatory reinterpretation, litigation, and statutory reevaluation surrounding Section 401. The proposed rule marks EPA’s third major reinterpretation of Section 401 in the last decade. Given the proposed rule’s implications for federalism, project timelines, and the scope of certifying authority conditions, and in light of recent limits on agency deference, legal challenges seem likely.

Next steps

EPA will host a public meeting with two sessions addressing the Proposed Rule on January 28, 2026. The sessions are open to states, Tribes, Section 401 applicants, and the public. The comment period ends February 17, 2026.